The advent of large-scale genomic sequencing is providing researchers with an unparalleled wealth of information which can be used to elucidate the evolutionary relationships of living organisms. The newly available genome sequence data have enabled the use of comparative genomic techniques for the identification of novel molecular signatures, shared uniquely by evolutionarily related groups of organisms: conserved signature indels (CSIs) and conserved signature proteins (CSPs). These signatures allow for the unambiguous delineation of the prokaryotic taxa, independent of gene and genome based phylogenetic trees, and provide insights into novel aspects of their evolutionary relationships. The phylum Spirochaetes and the class Betaproteobacteria are large, diverse groups of bacteria, containing many important pathogenic and environmental organisms, which are classified primarily on the basis of 16S rRNA gene analysis. Here, I describe phylogenetic analyses of the phylum Spirochaetes based on genome derived molecular signatures. These analyses have yielded substantial evidence for differentiation between the three main sequenced groups of organisms within the phylum Spirochaetes and between the genus Borrelia from other closely related Spirochaetes. These findings have prompted a proposal to create three new orders and a new family within the phylum. These analyses have also supported the differentiation of two clinically distinct groups within the genus Borrelia and a proposal to divide the genus Borrelia into two genera. The use of molecular signatures and phylogenetic analysis of major groups within the class Betaproteobacteria are also described. The analyses of the order Neisseriales within this class resulted in a division of the order into two families, while the analyses of the genus Burkholderia supported the differentiation of the clinically relevant members of the genus Burkholderia from the plant-beneficial and environmental Burkholderia and a proposal to divide the genus into two genera. I also describe the use of phylogenomic techniques and molecular signatures to differentiate the seven main groups within the order Enterobacteriales and the integrated software pipeline used to produce the supermatrix based phylogenomic tree and genome distance calculations in the analysis of the order Enterobacteriales. The molecular signatures described in this thesis represent powerful new tools for evolutionary and systematic studies. Additionally, due to their taxon specificity, these molecular signatures are novel diagnostic markers for their specified group. Further analyses of these molecular signatures should lead to the discovery of novel functions and biological characteristics, mediated by CSIs and CSPs, which will provide important insights into the physiology, evolution, and adaptations of these groups. / Thesis / Doctor of Philosophy (PhD)
| Identifer | oai:union.ndltd.org:mcmaster.ca/oai:macsphere.mcmaster.ca:11375/20596 |
| Date | January 2016 |
| Creators | Adeolu, Mobolaji |
| Contributors | Gupta, Radhey, Biochemistry and Biomedical Sciences |
| Source Sets | McMaster University |
| Language | English |
| Detected Language | English |
| Type | Thesis |
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